Using recordings of earthquakes on Oceanic Bottom Seismographs and onshore stations on the coastal margins of Colombia, Panama, and Ecuador, we estimate attenuation parameters in the upper lithosphere of the Panama Basin. The tomographic images of the derived coda-Q values are correlated with estimates of Curie Point Depth and measured and theoretical heat flow. Our study reveals three tectonic domains where magmatic/hydrothermal activity or lateral variations of the lithologic composition in the upper lithosphere can account for the modeled thermal structure and the anelasticity. We find that the Costa Rica Ridge and the Panama Fracture Zone are significant tectonic features probably related to thermal anomalies detected in the study area. We interpret a large and deep intrinsic attenuation anomaly as related to the heat source at the Costa Rica Ridge and show how interactions with regional fault systems cause contrasting attenuation anomalies.